Some metals such as nickel, aluminum and steel are ubiquitous in our daily lives, and can be found in coinage, cookware, bridges, and more. Other metals, known as “precious metals”, are rarer and more expensive—but if you’ve ever owned a smartphone or taken medication, then you’ve likely benefitted from them as well.
An average iPhone contains approximately 0.034 grams of gold and 0.34 grams of silver, as well as smaller amounts of rare Earth elements such as yttrium, terbium, and neodymium. Precious metals are also used in the large-scale syntheses of commercial drugs. A common example is palladium, which catalyzes “cross-coupling” reactions—in which two molecules are coupled together—used to prepare Losartan (to treat high blood pressure) and Diflunisal (to treat fever and pain).
The ability for scientist to develop new drugs for everything from rare diseases to headaches is often reliant on precedent and systematic investigations. These methods are often costly and time consuming. Similar problems arise in development of new materials that may enhance our energy production. Our limited ability to rationally design materials hampers their development. This leads to reliance on our ability to recognize the trends and behavior of already existing materials. However, what if we could amplify the ability to recognize patterns beyond human limits? Machine learning answers this problem.
A graph depicting the general algorithm machine learning follows. Source: Wikimedia Commons
While machine learning is a form artificial intelligence, our jobs are safe. Machine learning is the use of statistics and the power of computers to predict results or identify trends in data. The general method relies on the input of “training” data which is analyzed using statistics. After developing a model, information may be inferred from new data the computer encounters.
Large technology companies have recognized the advantage of integrating machine learning into technology development. Google is one example that has successfully introduced it. Gmail uses machine learning to service 1.5 billion active accounts. They claim to detect 99.9% of phishing and spam mail from entering the user’s inbox. However, machine learning is not limited to technology companies. Chemistry researchers have quickly adopted it.
Total Number of Chemistry Publications with “Machine Learning” in Title
Starting in 1969, the first chemistry journal article with “machine learning” in the title was published. By combining machine learning with a common technique called mass spectrometry, Peter Jurs at the University of Washington was able to determine chemical composition of “unknown” chemicals using the input of 348 unique patterns as “training” data.
More recently there has been an almost exponential increase in the number of chemistry publications applying machine learning. In the last two years approximately 6 times as many publications were made than in the past 48 years. Tommi Jaakkola, a Professor of Electrical Engineering and Computer Science at MIT said at a consortium about implementing machine learning in the pharmaceutical industry: “by marrying chemical insights with modern machine learning concepts and methods, we are opening new avenues for designing, understanding, optimizing, and synthesizing drugs.” The materials science community has also seen integration with the development of novel long chained molecules called polymers for photovoltaics by scientist at Osaka University. Shinji Nagasawa, the lead author explained the importance: “there’s no easy way to design polymers with improved properties. Traditional chemical knowledge isn’t enough. Instead, we used artificial intelligence to guide the design process.”
Solar cell efficiency over years showing a substantial increase. Source: Wikimedia Commons
While machine learning is not the solution to all chemical problems or spam mail, it is being widely accepted by the scientific community and technology industry for good reasons. Even with limitations, it’s effectiveness across a wide array of industry and research emphasizes the role it may play in the future of research and development.
—Jonah
References
Graph-powerd Machine Learning at Google. Google AI Blog. https://ai.googleblog.com/2016/10/graph-powered-machine-learning-at-google.html (Accessed Feb 28, 2019).
Jurs, P.C.; Kowalski, B.R.; Isenhour, T.L. Computerized Learning Machines Applied to Chemical Problems: Molecular Formula Determination From Low Resolution Mass Spectrometry. Chem. 1967, 41, 21-27.
Machine Learning, Materials Science and the New Imperial MOOC. Imperial College London. https://www.imperial.ac.uk/news/187054/machine-learning-materials-science-imperial-mooc/ (Accessed Feb 28, 2019).
Throughout history, both natural and synthetic opioid drugs have been considered popular therapy for chronic pain. However, their role as effective painkillers has been challenged by the potential for desensitization and addiction. Currently, the United States (U.S.) and Canada face an opioid crisis of epidemic proportions, with overdoses and related deaths attributed to prescription opioids (POs) as well as illicit, synthetic opioids.
This epidemic arose partly from an extensive history of over-prescribing practices. Many studies have suggested a link between PO availability and related mortality in both Canada and the U.S. Fortunately, the rise in reports connecting PO availability to mortality has been followed by a decrease in the number of opioid prescriptions, as seen in Figure 2 (2016 to 2017).
Figure 2. The Number of people prescribed an opioid. Source: CIHI
In the U.S., heroin, compared to any other single drug, is responsible for at least twice as many deaths. Alarmingly, in 2017, the number of people who have used heroin in their lifetime was over 5 million (seen in Figure 3).
Across Canada and the U.S., current treatment for opioid use disorder predominantly rests on replacement therapy with methadone or buprenorphine, which can help reduce withdrawal symptoms and maintain abstinence. Systemically, the reinforcement of regulations for PO has been attempted in parallel with the development of anti-abuse technology.
One promising anti-abuse strategy focuses on vaccination. Interestingly, one of the earliest attempts to reduce the misuse of psychoactive substances was reported in the 1970s, when a conjugate vaccine containing morphine-like hapten was tested in animal subjects. At the time, however, the emergence of Methadone, a pharmacotherapeutic for opioid ceased further development of this vaccine. Although drug conjugate vaccine research re-emerged in the 1990s, this time focused on cocaine and nicotine, limited success in human trials challenged the clinical value of this approach to substance abuse treatment—until now.
Learning from the failures of past attempts, a team of chemist and immunologists at The Scripps Research Institute recently developed an opioid vaccine candidate that neutralizes doses of heroin without any known side effects. In essence, the vaccine stimulates the immune system to produce antibodies that bind to heroin and block it from reaching the brain thus eliminating the euphoric high.
Their study was conducted on non-human primates, specifically four monkeys that were each given three doses of the vaccine. Following vaccination, the treatment countered heroin’s effects, and it continued to provide some degree of protection for more than eight months. Given that the components of this vaccine either have been approved by the FDA or have passed safety tests previously, the researchers believe that this candidate will prove safe in humans. In order to confirm, their next step involves licensing the vaccine to an outside company and establishing a partnership for future clinical trials. As we continue refining this vaccine against heroin, its progress can pave the road for the development of even more vaccines for other opioid synthetics, thereby expanding our approaches to substance abuse treatment.
Last year, chemical engineer Frances H. Arnold from the California Institute of Technology earned the 2018 Nobel Prize in Chemistry for her pioneering and brilliant work with the directed evolution of enzymes. She became the second female to win the prize in Chemistry.
Figure 1: The flowchart for the directed evolution of enzymes. Source: Advanced Information. NoblePrize.org. https://www.nobelprize.org/prizes/chemistry/2018/advanced-information/
Enzymes are biological catalysts to promote biochemical reactions in living organisms, and different enzymes specialize in different reactions. When the environment changes, genes mutate, and hence enzymes evolve to help an organism develop desired traits and adapt to the new environment. Although natural enzymes are excellent at doing their job, there are limitations: they only make chemicals that organisms need and only function in water at room temperature. These restrictions narrow the application of enzymes in the chemical and pharmaceutical industries. To tackle these problems, Dr. Arnoldhas used the same strategy as nature does-introduce mutations to existing enzymes-and obtained evolved enzymes which can quickly adapt to unusual environments, i.e., organic solvents, and speed up desired reactions. In the early 1990s, she reported the first case using subtilisin E, a digesting enzyme, to make an enzyme with much higher activity. This well-designed enzyme is 256 times more efficient to function the same reactions than the original enzyme in a polar organic solvent. This work has been seen as the benchmark achievement for the field of directed evolution of enzymes.
Figure 2: Reaction rate of hydrolysis of sAAPF-pna by subtilisin E variants in the solution containing 40% (vol/vol) DMF. Data source: Chen, K.; Arnold, F. H., Proc. Natl. Acad. Sci. USA, 1993, 90, 5681-5622
Dr. Arnold and her colleagues have been devoting to developing a variety of enzymes to deal with different synthetic challenges. For example, written in Nature this year, they describe a new iron-based enzymatic system to activate inert C-H bonds, replacing noble-metal catalysts. As the directed evolution proceeds, the system has a higher total turnover number (TTN) which represents how much product can be made until the catalyst is no longer active. Higher TTN means that the system becomes increasingly active as the enzyme evolves. The evolved enzyme CHF exhibits excellent stereoselectivity which is significant in pharmacology as human bodies react differently to enantiomers.
Figure 3: The bar chart represents the mean total turnover number (TTN) values averaged over four reactions; the grey dots show each TTN; green diamonds demonstrate enantioselectivity data. Source: https://www.nature.com/articles/s41586-018-0808-5
Another recent pioneering work done by Arnold group is using a natural enzyme to form C-Si bond which is unknown in nature although Silicon is the most abundant element in Earth’s crust. Silicon has extensive applications in chemistry and material science, including pharmaceutical developments and productions of semiconductors, and preparations of silicon-containing molecules, especially organic compounds, usually require multi-step and unsustainable synthetic routes. This innovative and environmentally friendly method offers new avenues of producing organosilicon compounds and opens up more opportunities in pharmaceutical research. These findings also shine the lights on what silicon-based life might look like, which has long been a fantasy in science fictions!
Figure 4: The active environment of the enzymatic system for C-Si bond formation Source: http://science.sciencemag.org/content/354/6315/1048
Figure 5: Artist rendering of Si-based life form Source: https://media3.s-nbcnews.com/j/newscms/2017_16/1969741/organosilicon-based-life_c18e68cad6b3bf817a28e03558a7bfba.fit-2000w.jpg
As a winner of the Nobel Prize, Dr. Arnold will encourage more people, especially women, to do science, and inspire more research in biocatalysis. As she pointed out in her essay, using well-functionalized enzymes rather than transition metals as catalysts allows for the development of sustainable chemical and pharmaceutical industries, and hence producing many of chemicals with biocatalysts will be the trend in the near future.
Dr. Arnold’s Nobel Lecture: Innovation by Evolution. Source: YouTube
References
Directed evolution, Wikipedia.org, https://en.wikipedia.org/wiki/Directed_evolution (accessed on Feb. 28, 19)
Typically, TV forensic shows, such as CSI and Bones, portray how forensic cases are fast and easy to solve within a couple of episodes. However, that is not true. Unlike in forensic shows, forensic cases take a long time to solve in real life, due to challenges that investigators have to face.
Currently, there are numerous studies that use different methods for solving the PMI. Many methods include analyzing soil chemistry and insects at the crime scene. Since these methods could be complementary to each other, the scientists in Switzerland believe that combining these methods would improve the long-term PMI estimate, while illustrating how the crime scene could have occurred. Therefore, the Swiss scientists have attempted to use five different approaches simultaneously to estimate the PMI of the bone and hair remains. Once the soil, bone, and hair samples are collected from the Swiss forest, the scientists use five different approaches for analyses, which include using radiocarbon dating, analyzing pH and soil chemistry, counting and classifying nematodes and mites, and sequencing DNA of soil micro-eukaryotes.
After analyzing the findings, the scientists are able to propose a possible PMI, as well as the crime scene. First of all, the radiocarbon dating determines that the bones belong to a young adult male. Secondly, chemical, nematodes, and micro-eukaryotic analyses suggest that the remains have been partly decomposed in the forest for at least 8-9 months. Finally, the evidence from mites suggests that the corpse is partly decomposed in a separate confined place, because these mite species are only found in confined environment. Therefore, the suspect(s) could have allowed the corpse to decompose in a confined area before relocating it to the Swiss forest. As a result, the PMI of the dead victim appears to be at least 8-12 months before the body is discovered.
The skeleton that is found in a Swiss forest. Ildikó Szelecz, Sandra Lösch, Christophe V. W. Seppey, Enrique Lara, David Singer, Franziska Sorge1, Joelle Tschui, M. Alejandra Perotti & Edward A. D. Mitchell, Source, Creative Commons Attribution 4.0 International Licence
Overall, the study shows that using five approaches simultaneously in a forensic case study can estimate the PMI, while illustrating a possible crime scene of how the victim could have died. Moreover, all of the approaches can be complementary with each other, in order to provide more evidence from scarce remains. In conclusion, it is possible to further develop this technique in order to estimate PMI in other forensic cases.
Update: Blog post has been revised on 2019, Feb 15th.
Szelecz, I.; Lösch, S.; Seppey, C. V. W.; Lara, E.; Singer, D.; Sorge, F.; . . . Mitchell, E. A. D. . Comparative analysis of bones, mites, soil chemistry, nematodes and soil micro-eukaryotes from a suspected homicide to estimate the post-mortem interval. Scientific Reports. [Online]2018,8(1), 25. doi:10.1038/s41598-017-18179-z.
Monosodium glutamate (MSG) is a crystalline powder that is widely used in the food industry as a flavour enhancer that intensifies the meaty/savoury flavour found in certain food items. It was discovered in 1908 by the Japanese chemistry professor Kikunae Ikeda, where he extracted MSG from seaweed. MSG is the sodium salt of glutamic acid (also known as glutamate), a non-essential amino acid that can be found in our bodies.
Photo source: BUSINESSINSIDER
MSG can either be synthesized or found in certain foods. These foods contain different amounts of glutamate. For example, Parmesan cheese, soy sauce, and fish sauce all contain more than 1000mg/100g of that food item. If you’ve ever wondered why these food items are so mouthwatering, this may be why!
Unfortunately, MSG is suspected of causing certain symptoms such as, headaches, heart palpitations, chest pain, nausea, and others. The substance first got its bad reputation when Robert Ho Man Kwok experienced abnormal heart rates, weakness, and numbness after eating excessive amounts of Chinese food. His colleague later decided that MSG was the cause of these symptoms without any scientific evidence. Further studies have since been done, for example, Ohguro et al. have done tests on rats before, the results showed damaged retina when 10 grams of sodium glutamate was added to a 100 gram diet. However, a simple search on the safety of ingesting MSG will result in find articles that state that there is no link between MSG and health hazards. Hence, the potential risks associated with MSG remain controversial. For now, MSG has been classified by the food and drug administration (FDA) as “generally recognized as safe.” This said, the FDA still requires manufacturers to label any food items that contain MSG.
To conclude, further studies need to be conducted to conclude whether MSG is a potential risk to one’s health. Although it may seem that there is a certain “catch” to flavour enhancers, our bodies can’t actually distinguish between naturally occurring glutamate and glutamate from MSG. As a matter of fact, today’s technology can’t differentiate between the two either. That being said, it is not a challenge to avoid food containing MSG for those that are concerned.
For more information on MSG, consider the following video:
Produced by the American Chemical Society
-Isabelle Lee
References
Center for Food Safety and Applied Nutrition. Food Additives & Ingredients – Questions and Answers on Monosodium glutamate (MSG). .https://www.fda.gov/food/ingredientspackaginglabeling/foodadditivesingredients/ucm328728.htm (accessed Jan 27, 2019).
Katherine Zeratsky, R. D. How does your body react to MSG? https://www.mayoclinic.org/healthy-lifestyle/nutrition-and-healthy-eating/expert-answers/monosodium-glutamate/faq-20058196 (accessed Jan 27, 2019).
Bright Tribe, I. Glutamate in Food – The Glutamate Association https://msgfacts.com/glutamate-in-food/ (accessed Jan 27, 2019).
The Truth in Labeling Campaign is all about knowledge. https://www.truthinlabeling.org/ (accessed Feb 14, 2019).
There a few interesting phenomena that occur once we get to near 0 K temperature. One of these interesting phenomena is superfluid. A popular example of a superfluid material is liquid helium near 0K. Both isotopes of helium 3He and 4He can form super fluid at very low temperatures. Superfluidity is characterized by having 0 or almost zero viscosity, meaning that the fluid can move upon a surface without losing kinetic energy. A superfluid vortex would last forever.
Liquid helium earns superfluid properties once its temperature goes under a temperature called the lambda point. These properties were first discovered in 1937 by Pytor Kapitsa, who published a paper about it in January 1938. While he was attempting to measure the thermal conductivity of liquid helium, he was running the liquid through a gap between two discs and measured the flow rate of the liquid. He noticed that the flow increased rapidly after going below a certain temperature. The flow rate of the superfluid helium also does not change as a function of pressure, and no viscosity formula at the time was able to give a tangible value for its viscosity.
There is a behaviour that is observed in superfluids that has yet to be adequately explained. As seen in the video if you have a superfluid in a cup the fluid can flow up against gravity and climb up the wall of the glass. The extremely low viscosity helps explaining the phenomenon, but still doesn’t help explaining it fully. An interesting thought that emerges after observing this behavior is that if we have a superfluid fountain it would flow forever without the need of external forces.
Superfluidity is just one of the interesting properties that can be observed near 0 K, having 0 viscosity allows for a lot of crazy behaviors such as: an infinitely flowing fountain, and a vortex that keeps on rotating forever. This property, along with other properties like superconductivity, shows that with just manipulating temperature a whole new range of possibilities open up.
We all are familiar with coffee, whether we drink it or not. The 2018 Coffee Association of Canada Study states that 72% of Canadians aged 18-79 drank coffee yesterday. Often, we think coffee is a source of addiction for its nice taste and a stimulating sensation. Others make efforts to withdraw from drinking too much because of the toll it takes on their health. We rarely think coffee will disappear because it sounds so abundant. Yet we don’t realize that coffee is leading towards extinction faster than we think.
Coffee cultivation is significantly decreasing due to human activities. Deforestation and fossil fuel usage have raised temperatures, affecting the quality and quantity of coffee production. In addition, diseases such as coffee rust eat up the leaves and negatively impacts the coffee plantations. While it is not an immediate concern, a computerized climate model predicted that wild Arabica could go extinct by 2080. Despite the concerns shown by the industry and researchers, there is no commercial genetically modified (GM) coffee. However, there have been efforts in research to develop GM coffee, in hopes of a longer lifetime.
Predicted climate change outcomes for indigenous Arabica localities for one emission scenario. Source
Researchers used genetic engineering to introduce herbicide resistant coffee plants, a method to decrease weed damage while reducing phytotoxicity. In a Coffea canephora P study, researchers produced a genetically transformed coffee, by a particle bombardment of a DNA plasmid pCambia3301. Both transformed and non-transformed leaves were sprayed with herbicide ammonium glufosinate in greenhouse conditions. The non-transformed leaves showed clear signs of darkening and wilting, but the transformed leaves stayed in good condition.
One week after transformed leaves (A) and non-transformed leaves (B), sprayed with herbicide ammonium glufosinate. Source
Geneticist Juan Medrano from UC Davis College released the first public sequenced genome of Coffee Arabica in 2017. He hopes that not only researchers but also coffee consumers and farmers can use this information. Modifications to the sequence can give new insights to combat environmental stresses and infections. In addition, introducing new flavors and fragrances can keep Coffee Arabica’s quality.
Although genetically modified coffee technology is already available, many consumers remain skeptical regarding their consumption. This is due to their nature as chemically treated foods, also known as “Frankenfoods”. Because of human impact on the Earth and Mother Nature’s response, it is inevitable that genetically modified foods will slowly dominate the food industry. Time goes by quicker than we think, so take a moment to cherish the natural coffee while it lasts.
Global temperature averages are increasing at abnormal rates. Sea levels are rising, ice caps are melting, and nature is dying. Almost all governments and scientists worldwide have been looking for solutions to impede the fate that humanity is heading towards. One of the ways is through using a cleaner energy source such as hydroelectricity.
In the past two decades, hydroelectricity has become more popular as a substitution for fossil fuel powered energy production. Its claim to fame was that it was a clean way to generate electricity; it was a viable solution for the future as climate change started to become a mainstay in the news. Initial studies had hydroelectricity being almost emission free!
Vattenfall Study for Carbon Emissions of Fossil Fuels, Renewables, Nuclear. Source: Wikimedia Commons
When thinking about producing electricity using water, one would think of it as being a clean and renewable process. It’s water! People bathe in it and drink it. How can it be dirty?
Unlike coal, a non-renewable resource which takes millions of years to form, the water isn’t being burned or used up. However, like coal , it is not clean (albeit to a much lesser extent).
The basics of hydro-power is that water is pumped through a turbine to induce spinning. This motion activates a generator, producing the electricity which has become so important in daily life. The dirty part comes from the carbon emissions generated during construction and passively during the hydroelectric dam’s lifetime.
Throughout the building process, many carbon sinks will be destroyed as trees and plants will be chopped down. This reduces the overall carbon dioxide that can be stored while releasing the carbon dioxide back into the atmosphere. Not to mention the habitats and the environments near the power plants that are destroyed at the same time.
However, it’s not just during the initial construction that hydroelectric power is unclean. Plants and other living things are able to grow in these bodies of water. All living things that die and decompose in the waters produce methane, carbon dioxide, and nutrients. The nutrients in turn help other living organisms grow, thus continuing the cycle. When thought about in this manner, the hydroelectric dams become carbon emission generators.
In its current state, hydroelectricity is not a clean source of power. Nevertheless, it is a viable alternative to fossil fuels as we transition to better solutions. There is hope in the future that hydro-power becomes one of these solutions. Companies are still innovating and working towards a setup that is gentler on the environment while still providing adequate amounts of electricity.
You wake up in the morning and then press snooze on your alarm clock one more time before groggily dragging yourself out of bed to the bathroom. Quickly you brush your teeth with your electric toothbrush, then hop in the shower and lather yourself with the bottle of that fancy body wash with the microbeads in it. In the kitchen, you grab the lunch you made from the prepackaged salad mix before heading out the door. Now in your car, you turn some knobs on the dashboard to play some music on your way to work or school. In case you have lost count, you have already encountered half a dozen plastic products and it isn’t even 9 AM yet.
Plastics are the result of taking petrochemical monomers (such as ethylene) and converting them to long chain polymers. This is done through a process called polymerization which is relatively easy and cheap to do. Another process, called photo-oxidation occurs as a result of exposure of these long-chain polymers to UV radiation (from the sun) and oxygen (in the air). Essentially, this process causes plastics to become brittle and in combination with the elements (wind and water abrasion), causes the degraded plastics to break into minuscule pieces. When these pieces are between 0.1 and 1000 μm in size, they are referred to as microplastics.
Due to plastics being such a cheap and omnipresent resource, there has been little incentive to recycle such products, leading to an accumulation of plastic waste in landfills and the world’s oceans. It is tragic to see seawater bodies filled with plastic, but only recently has it come into light that these microplastics are starting to make their way into our own bodies too. While seemingly obvious, microplastics have been reported in seafood, but they are also found in fertilizers and in common food items such as beer, sugar and salt. One study from last year found microplastic particles in 17 salt brands from 8 different countries. Additionally, atmospheric fallout of microplastics has also been reported, so it’s very possible we have already been inhaling and consuming microplastics.
A (a) polyisoprene/polystyrene, (b) polyethylene, and (c) pigment (phthalocyanine) fragment. Image (d) is a nylon-6 filament. Source
So what can be done to mitigate the amount of plastic that is becoming ocean waste and effectively microplastics? Our daily lives and plastic products have become too intertwined to even entertain the thought of completely banning plastics worldwide. Fortunately, there have already been movements to ban especially harmful products such as microbeads found in many skin products. But, some effective steps that everyone can implement into their routines are to reduce the use of single-use plastics such as plastic straws or plastic grocery bags. The issue with single-use or “disposable” plastics is that they are difficult to recycle and thus only contribute to plastic waste. Additionally, choosing products that have less plastic packaging is also a viable way to lessen your plastic consumption. Lastly, whenever possible, recycle your plastic products so your plastic water bottle can become a new plastic water bottle and not the microplastics in our food.
The following video is a collaboration between BBC Earth Lab and Exeter University and shows how microplastics can make it through the food chain and potentially onto our plates.
